The goal of this project is to develop a method to monitor the expression levels of a large number of genes in various experimental conditions and to elucidate the global structure and behavior of a gene regulatory network in development and aging. In our previous work, we have constructed cDNA libraries from early mouse embryos and stem cells and generated a large number of expressed sequence tags (ESTs). During the last one-year period, we have accomplished the following additional goals. 1) We have developed a glass-slide microarray platform containing in situ-synthesized 60-mer oligonucleotide probes representing approximately 44,000 unique mouse transcripts. 2) We have produced web-based ANOVA-FDR software to provide user-friendly microarray data analysis too. 3) We have developed an algorithm and a fully-automated computational pipeline for transcript assembly from expressed sequences aligned to the mouse genome. We have identified 191,946 genomic loci, which included 27,497 protein-coding genes and 11,906 additional gene candidates (e.g., non-protein-coding, but multi-exon). 4) We have developed a high throughput whole-mount in situ hybridization technique for preimplantation mouse embryos and ES cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.